Every time you want to access pear you have to type "/Applications/MAMP/bin/php5.3/bin/pear". Typing "pear" referes to what is installed on your mac already and not MAMP's install. (This only apply for the current session. For a more permanent alias see http://clarksco.com/?p=32)

Pear gets confused about its version because it installs in both php5.3 and php5 directory

When you upgrade pear it will create a new /Application/MAMP/bin/php5 directory and spread files between php5.3 and php5 folders. Use the code below to make a link between the two file so they act as one. More info about "ln" command. Source: @Marcelo Rodrigo's post